Alignments for a candidate for nagEcb in Lentibacillus jeotgali Grbi

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagEcb in Lentibacillus jeotgali Grbi

Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate WP_010529795.1 ON01_RS04430 PTS transporter subunit EIIC

Query= reanno::BFirm:BPHYT_RS02745
         (591 letters)



>NCBI__GCF_000224785.1:WP_010529795.1
          Length = 492

 Score =  353 bits (905), Expect = e-101
 Identities = 205/493 (41%), Positives = 290/493 (58%), Gaps = 42/493 (8%)

Query: 9   IQRLGRALMLPIAVLPVAGLLLRLGQ-------PDVFNIKMIADAGG-AIFDNLPLLFAI 60
           +Q LGR+LMLP+AVLP A +L+ + +            I    ++GG AI DNL +LFA+
Sbjct: 5   LQNLGRSLMLPVAVLPAAAILVGISKYIEKIDGTTAGTIATFLNSGGLAILDNLGILFAV 64

Query: 61  GVAVGFAKDNNGVAGLAGAIGYLIEVAVMK-------------DINDKLN--MGVLSGIV 105
           GVA+G +K+ +G AGL+G + +L+   V+               +N        V  GI+
Sbjct: 65  GVAIGMSKEQDGAAGLSGLVAWLVATTVLSVSGVAGLQGIEESAVNPAFENIQNVFIGIL 124

Query: 106 AGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAG 165
           +GIVA ++YNR+  ++LPD LAFF GKR VPI++    +V+ +   +VW  V   + + G
Sbjct: 125 SGIVASIMYNRFSHVRLPDALAFFSGKRLVPIMSAASMMVVSVLLLFVWPVVYNALVSFG 184

Query: 166 HWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGD 225
             + +  A+GA ++G LNRLL+ TGLHH LNS+ WF           A   D+  F+A +
Sbjct: 185 EAIISLEAVGAGIYGFLNRLLIPTGLHHALNSVFWF---------DVAGIDDIASFWASE 235

Query: 226 P---TAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPI 282
                 G ++ GFFP+MMFGLPAA LAM+H A  +R+     LL + A  SF TGVTE +
Sbjct: 236 GEKGVTGRYLAGFFPIMMFGLPAAALAMYHTAKTKRKKQAASLLMAAAFASFFTGVTEAL 295

Query: 283 EFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYG--LSTRGWWAI 340
           EFSFMF+APVLYV+HA LTG+SLA+ +      GF+FSAG +DY L+ G  ++ + +  I
Sbjct: 296 EFSFMFVAPVLYVVHAALTGLSLAVAAMFEWTAGFSFSAGLVDYTLSLGIPIANQPYMLI 355

Query: 341 PIGLVYMVVYYGLFRFFIRKFNMATPGREPAAADE-QVD---SFAAGGFVSPVAGTAVPR 396
             GLV+ V+YY LFRF I K ++ TPGRE     E +VD   +   G   S    TAV  
Sbjct: 356 LQGLVFAVLYYFLFRFLIVKLDLNTPGRESDEPGEGEVDESYNVEEGTLASEKDETAV-M 414

Query: 397 AQRYIAALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIG 456
           A+     LGG  N+  VD C +RLRL V D +KV ++++K  G  GV   G  NVQV++G
Sbjct: 415 AEEIYQGLGGDENVRTVDNCVSRLRLEVDDMDKVDQDKIKATGVPGVNVVGKHNVQVVVG 474

Query: 457 PEADIIADEIRTV 469
            +   +ADEIR +
Sbjct: 475 TQVQFVADEIRKI 487


Lambda     K      H
   0.325    0.141    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 824
Number of extensions: 46
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 591
Length of database: 492
Length adjustment: 35
Effective length of query: 556
Effective length of database: 457
Effective search space:   254092
Effective search space used:   254092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources